Nature - 2019.08.29

9

nature research | reporting summary

October 2018

Res_BORIS_vs_Res_input_peaks_blacklisted.narrowPeak 17035

Res_BRD4_vs_Res_input_peaks_blacklisted.narrowPeak 26297

Res_CTCF_vs_Res_input_peaks_blacklisted.narrowPeak 58724

Res_JQ1_BORIS_vs_Res_JQ1_input_peaks_blacklisted.narrowPeak 12674

Res_JQ1_BRD4_vs_Res_JQ1_input_peaks_blacklisted.narrowPeak 9702

Res_JQ1_CTCF_vs_Res_JQ1_input_peaks_blacklisted.narrowPeak 37791

Res_narrow_Pol2_vs_Res_input_peaks_blacklisted.narrowPeak 54174

Res_MYCN_vs_Res_input_peaks_blacklisted.narrowPeak 6500

Software Fastqc (v0.11.5), STAR (v2.5.1b_modified), Samtools (v1.3.1), MarkDuplicates (v2.1.1), deepTools (v2.2.4), MACS2 (v2.1.1),

bedGraphToBigWig (v4), R (v3.5.1), Rstudio (v1.1.463), data.table (v1.12.2), trimmomatic (v0.36), HiC-Pro (v2.10.0),

hichipper (v0.7.3), diffloop (v1.10.0), ROSE (v1), Circlize (v0.4.5), IGV (v2.3.74). Custom code is available upon reasonable

request.

Flow Cytometry

Plots

Confirm that:

The axis labels state the marker and fluorochrome used (e.g. CD4-FITC).

The axis scales are clearly visible. Include numbers along axes only for bottom left plot of group (a 'group' is an analysis of identical markers).

All plots are contour plots with outliers or pseudocolor plots.

A numerical value for number of cells or percentage (with statistics) is provided.

Methodology

Sample preparation Flow cytometry was used for cell cycle analysis in both parental and resistant cells using propidium iodide (PI) staining. After

fixation of 1x10e6 cells overnight at 4C with 80% ethanol, cells were resuspended in PBS supplemented with 0.1% Triton X-100,

25 mg/ml PI, and 0.2 mg/ml RNase A, and incubated for 45 min at 37C in the dark before analysis.

Instrument Samples were run on a FACSCalibur flow cytometer (BD Biosciences).

Software Data collection was done with BD CellQuest Pro software (BD Biosciences), and analysis was performed using FlowJo software

(v10.0.5).

Cell population abundance No FACS sorting was performed for this work.

Gating strategy Cell debris as well as non-singlets were excluded by a gate based on FSC-H and SSC-H.

Tick this box to confirm that a figure exemplifying the gating strategy is provided in the Supplementary Information.